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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaatgttgtacttagttttgtttattttctgtcacttctagatttattgctttccttttcattagctggctcctgtccatatcatcatatgtctgttctcgaacaaatcatggccaaccattcgttacctgcagttaacaaaaccaagatattgttttgcttatattttcttttgtttattctgaaagCCTGGAGAATCACTGAGAGATTTCTACAAGAGGACAAATATGTACTGGCAAATGGCTGCCTATGAGCACACTCAACACACTGGAAAG

Basic information

species Zea mays
transcript GRMZM2G100815_T01
intron # 14
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G100815_T01 (Zea mays), 3'ss of exon 14
lower sequence: LOC_Os04g40740.3 (Oryza sativa), 3'ss of exon 9
gtaatgttgtacttagttttgtttattttctgtcacttctagatttattgctttccttttcattagctggctcctgtccatatcatcatatgtctgttctcgaacaaatcatggccaaccattcgttacctgcagttaacaaaaccaagatattgttttgcttatattttcttttgtttattctgaaagCCTGGAGAATCACTGAGAGATTTCTACAAGAGGACAAATATGTACTGGCAAATGGCTGCCTATGAGCACACTCAACACACTGGAAAG
|| |||||||| | |   ||     |||| |||    |||| |||| ||        || |   |          || |||||  |    ||| |  ||  ||  || || ||||  |  ||| |||||   ||||||||||    || |   | | |  || ||  |  | | |    | | | |||||| ||||| ||||| | ||||||||||||||| ||  ||||||||||||| |||||||| |||||||||||||||||||||||||||
gtgatgttgtaatcaacatt-----ttttttgt----tctaaatttgtttgaagttgttccgacaaa--------gtacatatactt---tgtttactca-gaggaactcttggctgataatttgttacacacagttaacaa--ttaaaaccatatatcactaat--tcccatattcacacttttaaagCCAGGAGAGTCACTAAAAGATTTCTACAAGAGAACGGATATGTACTGGCAGATGGCTGCATATGAGCACACTCAACACACTGGAAAG

upper sequence: GRMZM2G100815_T01 (Zea mays), 3'ss of exon 14
lower sequence: GLYMA04G36770.1 (Glycine max), 3'ss of exon 17
gtaatgttgtacttagttttgtttattttctgtcacttctagatttattgctttccttttcattagctggctcctgtccatatcatcatatgtctgttctcgaacaaatcatggccaaccattcgttacctgcagttaacaaaaccaagatattgttttgcttatattttcttttgtttattctgaaagCCTGGAGAATCACTGAGAGATTTCTACAAGAGGACAAATATGTACTGGCAAATGGCTGCCTATGAGCACACTCAACACACTGGAAAG
                                                                          | ||    |  |||| || ||    |  |||  |||    |    | |||   |   | | ||  |    ||     | |||||| |||| |||   || |  ||      |||||| ||||||||  |||  |||||||||| | | ||||||||||| ||||||||||| ||| |||| || ||||||||||||||||| 
-------------------------------------------------------------------------gtatctg-gttgtcatgtgcct----ttaaacgcatct---ctgggctttca--attagtatttttcttgtcc----cactgtttt-ctta-attgaattcttgttgcatccaaagCCAGGAGAATCCTTGAAGGATTTCTACAGGCGTACAAATATGTATTGGCAAATGGCAGCCCATGAACATACTCAACACACTGGAAAA

upper sequence: GRMZM2G100815_T01 (Zea mays), 3'ss of exon 14
lower sequence: AT5G50310.1 (Arabidopsis thaliana), 3'ss of exon 17
gtaatgttgtacttagttttgtttattttctgtcacttctagatttattgctttccttttcattagctggctcctgtccatatcatcatatgtctgttctcgaacaaatcatggccaaccattc-gttacctgcagttaacaaaaccaagatattgttttgcttatattttcttttgtttattctgaaagCCTGGAGAATCACTGAGAGATTTCTACAAGAGGACAAATATGTACTGGCAAATGGCTGCCTATGAGCACACTCAACACACTGGAAAG
                                                                                        || |  |||  |||       |||  ||    |||| |||  |||     |  | |  |    |   | |   || || |  || | |  || |  |  |||||||||||| |  |||  |||||||| ||| | ||||||||||||||||||||||||||||| ||||| || ||||| ||||| |||
---------------------------------------------------------------------------------------gtaagattgtcttcg------ccatttccttttattctgttgtctgaga--aggagattctgtttgaagctcaactaatttggtcatgttgttgtctttgaagCCTGGAGAAACTTTGAAGGATTTCTATAAGCGCACAAATATGTACTGGCAAATGGCTGCCTACGAGCATACCCAACATACTGGCAAG

upper sequence: GRMZM2G100815_T01 (Zea mays), 3'ss of exon 14
lower sequence: Vv17s0000g10130.t01 (Vitis vinifera), 3'ss of exon 17
gtaatgttgtacttagttttgtttattttctgtcacttctagatttattgctttccttttcattagctggctcctgtccatatcatcatatgtctgttctcgaacaaatcatggccaaccattcgttacctgcagttaacaaaaccaagatattgttttgcttatattttcttttgtttattctgaaagCCTGGAGAATCACTGAGAGATTTCTACAAGAGGACAAATATGTACTGGCAAATGGCTGCCTATGAGCACACTCAACACACTGGAAAG
                                                                                | |  |  | ||  | |    | |||  | |   |||  | ||  | | || ||   | ||  ||   |  |     ||||||||     | ||||| | || |||| |||||||||| |  |||  || ||||| ||| | || ||| |||||||||||||||| ||  ||||||||||||||||||||||||||
--------------------------------------------------------------------------------ttttgtgttgtgcatctaaaggcacatttaaactccattcttt--tcatct-catccatcattactttgtcaactgattgcttat-----catttgtattttgtgaa-gCCTGGAGAAACCTTGAAGGACTTCTATAAGCGTACCAATTTGTACTGGCAAATGGCAGCACATGAGCACACTCAACACACTGGAAAG

upper sequence: GRMZM2G100815_T01 (Zea mays), 3'ss of exon 14
lower sequence: PP1S15_393V6.2 (Physcomitrella patens), 3'ss of exon 18
gtaatgttgtacttagttttgtttattttctgtcacttctagatttattgctttccttttcattagctggctcctgtccatatcatcatatgtctgttctcgaacaaatcatggccaaccattcgttacctgcagttaacaaaaccaagatattgttttgcttatattttcttttgtttattctgaaagCCTGGAGAATCACTGAGAGATTTCTACAAGAGGACAAATATGTACTGGCAAATGGCTGCCTATGAGCACACTCAACACACTGGAAAG-------------
                    ||   |   || | | ||  | ||||||   | |||   | ||  ||||   |||||  | |     |||      || |  ||| || | | |   |   |||||| |       | ||   | ||| ||         || | |||    |    | | |     |||| ||||||    |||  ||||| |      | ||||| ||||| ||||||||||| ||||| |||||||||||||| ||||| ||              
--------------------gtacgtgcactattagttg-acatttatgtttctccggcttatctgctg---cctgtaaagagggggata-----atttttcaacgaagc-tagtttat--ttcgtttctca----ttactggagcaacatga------actgacattagaatgaaatgactgc---agCCAGGAGAAAGCTTGAAGGATTTTTTTGCTCGAACAAACATGTATTGGCAAATGGCAGCCTACGAGCACACTCAACATACTGGCAAAGAACTACGGAAGG

upper sequence: GRMZM2G100815_T01 (Zea mays), 3'ss of exon 14
lower sequence: EFJ11619 (Selaginella moellendorffii), 3'ss of exon 15
gtaatgttgtacttagttttgtttattttctgtcacttctagatttattgctttccttttcattagctggctcctgtccatatcatcatatgtctgttctcgaacaaatcatggccaaccattcgttacctgcagttaacaaaaccaagatattgttttgcttatattttcttttgtttattctgaaagCCTGGAGAATCACTGAGAGATTTCTACAAGAGGACAAATATGTACTGGCAAATGGCTGCCTATGAGCACACTCAACACACTGGAAAG
                                                                                                                                   |    | |  | |  |    ||  | | | ||     |  | ||| ||  |||   ||||||| ||| | ||||||||||| | |    |||| |  ||||| |||||||||||||| || || ||||| |||||||||||||||
-----------------------------------------------------------------------------------------------------------------------------------gtgagtgatgatagtagtccatcttctcgttt-----tgttattgatttgtcttccagCCTGGGGAAACGCTGAGAGATTTTTTCTCCCGGACGATCATGTATTGGCAAATGGCTGCTTACGACCACACCCAACACACTGGAAAG

Mapped EST sequences

Showing partial alignments of ESTs and genomic sequences. See full alignments


 ATGC     EST sequence
 ATGC     genomic sequence (exon)
 ATGC     genomic sequence (truncated intron)


EST: gi|60351145|gb|DN218118.1|DN218118
EST:     AACAGATCAGGGTCATCCTTGGCCTTTCTGATTCTCAAAGGACTCCAGTG                         CCTGGAGAATCACTGAGAGATTTCTACAAGAGGACAAATATGTACTGGCAA
genomic: AACAGATCAGGGTCATCCTTGGCCTTTCTGATTCTCAAAGGACTCCAGTGgtaatgttgt ... attctgaaagCCTGGAGAATCACTGAGAGATTTCTACAAGAGGACAAATATGTACTGGCAA
EST: gi|148980754|gb|EE027321.2|EE027321
EST:     AACAGATCAGGGTCATCCTTGGCCTTTCTGATTCTCAAAGGACTCCAGTG                         CCTGGAGAATCACTGAGAGATTTCTACAAGAGGACAAATATGTACTGGCAA
genomic: AACAGATCAGGGTCATCCTTGGCCTTTCTGATTCTCAAAGGACTCCAGTGgtaatgttgt ... attctgaaagCCTGGAGAATCACTGAGAGATTTCTACAAGAGGACAAATATGTACTGGCAA

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 4 RNA-Seq libraries.


Block sizes: 45 (upstream exon), 49 (downstream exon)
Score: 101

GAAGGGTGAAAGTAAGACCATGCGTAGAAAAGAGAAGCGTGCTCGGATAGAACAGATCAGGGTCATCCTTGGCCTTTCTGATTCTCAAAGGACTCCAGTGgtaatgttgt ... attctgaaagCCTGGAGAATCACTGAGAGATTTCTACAAGAGGACAAATATGTACTGGCAAATGGCTGCCTATGAGCACACTCAACACACTGGAAAG


Block sizes: 48 (upstream exon), 48 (downstream exon)
Score: 58

GAAGGGTGAAAGTAAGACCATGCGTAGAAAAGAGAAGCGTGCTCGGATAGAACAGATCAGGGTCATCCTTGGCCTTTCTGATTCTCAAAGGACTCCAGTGgtaatgttgt ... attctgaaagCCTGGAGAATCACTGAGAGATTTCTACAAGAGGACAAATATGTACTGGCAAATGGCTGCCTATGAGCACACTCAACACACTGGAAAG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 48

GAAGGGTGAAAGTAAGACCATGCGTAGAAAAGAGAAGCGTGCTCGGATAGAACAGATCAGGGTCATCCTTGGCCTTTCTGATTCTCAAAGGACTCCAGTGgtaatgttgt ... attctgaaagCCTGGAGAATCACTGAGAGATTTCTACAAGAGGACAAATATGTACTGGCAAATGGCTGCCTATGAGCACACTCAACACACTGGAAAG


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 51

GAAGGGTGAAAGTAAGACCATGCGTAGAAAAGAGAAGCGTGCTCGGATAGAACAGATCAGGGTCATCCTTGGCCTTTCTGATTCTCAAAGGACTCCAGTGgtaatgttgt ... attctgaaagCCTGGAGAATCACTGAGAGATTTCTACAAGAGGACAAATATGTACTGGCAAATGGCTGCCTATGAGCACACTCAACACACTGGAAAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gttaacaaaaccaagatattgttttgcttatattttcttttgtttattctgaaagCCTGGAGAATCACTGAGAGATTTCTACAAGAGGACAAATATGTACTGGCAAATGGCTGCCTATGAGCACACTCAACACACTGGAAAG
 agttaac  putative branch site (score: 51)
                                ttttcttttgtttatt  putative PPT
                     ttttgcttatattttc  TA-rich tract